Bradford replied through Danny Cadamarteri but the Gills held on to record their sixth consecutive league win for the first time since October 1982.
A dour opening was enlivened when Gillingham went ahead after nine minutes. Matthew Jarvis raced down the left and twisted past John Swift before laying the ball across the face of goal for Black to sidefoot home from three yards out.
The home team piled on the pressure after the goal and Jarvis especially was causing the Bradford defence all sorts of problems.
They could have doubled their lead after 20 minutes but Alan Pouton hit clean air instead of the ball from only eight yards out.
Having not been at the races during the opening stages, Bradford were nearly level on 23 minutes.
Mark Bridge-Wilkinson's corner from the left was met by a powerful header from Mark Bower but Danny Jackman prevented the certain goal by clearing off the line. Two minutes later and the reverse happened but this time Swift blocked Andrew Croft's goalbound header from Black's corner.
Gillingham continued to dominate after the break and it came as no surprise when they doubled their advantage on 53 minutes.
Jackman's clever lobbed pass put substitute Flynn clear inside the penalty area and his left-footed volley gave Ricketts no chance.
Against the run of play Cadamarteri grabbed his first goal since August on 73 minutes as he out-muscled Brent Sancho before firing past Jason Brown.
Suddenly Bradford found their second wind and they could have snatched an improbable point with 10 minutes remaining when Dean Windass fired straight at Brown from point-blank range.